def test_dense_coverage(self):
reads = [
self.mock_read(range(0, 5)),
self.mock_read(range(0, 5)),
self.mock_read(range(1, 6)),
self.mock_read(range(2, 7)),
self.mock_read(range(3, 8)),
self.mock_read(range(1, 8))
]
pileup = _read.pileup(reads)
expected = list(zip(range(1, 9), [2, 4, 5, 6, 6, 4, 3, 2]))
self.assertEqual(expected, pileup)
def test_filter_reads(self):
reads = [
self.mock_read(range(0, 5), mapping_quality=0),
self.mock_read(range(0, 5), mapping_quality=0),
self.mock_read(range(1, 6), mapping_quality=0),
self.mock_read(range(2, 7), mapping_quality=0),
self.mock_read(range(3, 8), mapping_quality=10),
self.mock_read(range(1, 8), mapping_quality=10),
]
pileup = _read.pileup(reads, filter_func=lambda x: True if x.mapping_quality < 1 else False)
expected = list(zip(range(2, 9), [1, 1, 2, 2, 2, 2, 2]))
assert pileup == expected
def test_sparse_coverage(self):
reads = [self.mock_read(range(0, 5)), self.mock_read(range(20, 25))]
pileup = _read.pileup(reads)
expected = [(r, 1) for r in range(1, 6)] + [(r, 1)
for r in range(21, 26)]
self.assertEqual(expected, pileup)